use `plink --rel-cutoff` to remove related samples

Question

[blueskypie]

In the plink --rel-cutoff option, the default value for genomic relateness is 0.025. How does this genomic relateness value correspond to the degree of relationship or the PI-HAT?

Thanks for any help!

Answer 1

[chrchang523]

It is the relationship coefficient described in the GCTA paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3014363/

Note that plink 2.0's --king-cutoff function is a more reliable way to prune close relationships, since it doesn't require good population allele frequencies.

[seta]

Hi chrchang523,

Although it's late, I read the corresponding paper; but the question is still remaining. Could you please let me know which value should be selected for --rel-cutoff for removing related individuals with 2th degree of relationship?

Thanks

[Kevin Blighe]

For second degree relatives, may switch to KING (--king-cutoff). See relationship between PI_HAT and --king-cutoff coefficient?